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In standard orbit around an iron-silica-type uncharted planet, the USS Enterprise prepares to complete its survey, when the starship is violently rocked twice and everything within sensor range suddenly "blinks", almost as if the universe is on the verge of ceasing to exist. And, in the wake of this, a man appears on the surface of the planet, where moments earlier there was no life.

Beaming down, CaptainKirk, Spock, and the landing party encounter a man. "You came! Thank the heavens, it's not too late!", he exclaims. Dirty and disheveled, he falls from a rock. The landing party returns to the Enterprise with him, where Kirk learns more news – the strange phenomenon drained the dilithium crystals almost completely. Still worse, Starfleet Command issues a Code Factor 1 message – invasion status. The effect experienced by the Enterprise was also experienced everywhere in the galaxy, and far beyond. Starfleet withdraws all nearby ships – CommodoreBarstow informs Kirk that the Enterprise is the bait.

In his quarters, Kirk talks to his "guest" – a man named Lazarus, who is pursuing a "thing," a monster who destroyed his entire civilization. He informs Kirk that he will stop at nothing to destroy it. Beaming back down to the planet, Kirk learns from Spock that there is no other creature here. Spock, accusing Lazarus of lying, states "I fail to comprehend your indignation, sir. I have simply made the logical deduction that you are a liar." Kirk demands the truth – and the universe turns inside out once again. The same "winking" phenomenon occurs again. And Lazarus... first he has a bandaged forehead, and then he doesn't, and then he does again.

Meanwhile, Spock has discovered a source of radiation that is not there – a "rip" in the universe, where regular physical laws do not apply. The key to locating this source seems to be the dilithium crystals – a revelation which excites Lazarus, who demands the impossible: that Kirk give him the crystals.

The captain refuses, but Lazarus overpowers LieutenantCharlene Masters as well as an engineering officer and steals two dilithium crystals, nevertheless.

In the briefing room, Kirk confronts Lazarus, but he denies it, blaming his monster. And the evidence suggests he isn't the thief, for the crystals are not aboard his ship. In Sick Bay, Kirk confronts Lazarus with his lies, and learns that Lazarus distorted a fact: he is a time traveler. The dead world the Enterprise orbits is the distant future of his destroyed homeworld; the place and time he has traveled to in pursuit of the monster. At Dr. McCoy's urging, the crew departs Sick Bay to allow Lazarus to rest and recover from his fall.

Having relocated to the briefing room to consider all of the known evidence, Kirk and Spock conclude that the strange energy must come from a source outside the universe. A source in another, parallel universe. There are two copies of Lazarus, and they are periodically exchanging places through a kind of door – and if they ever exist in the same universe at the same time, everything, everywhere, will be annihilated in a cataclysmic matter/antimatter explosion.

Meanwhile, the alternative Lazarus creates a diversion by starting a fire in main engineering, steals the ship's energy crystals, then beams down. Kirk pursues. As he attempts to enter Lazarus' spaceship, he vanishes, hurled through the corridor into the other universe.

Once there, Kirk meets the other but sane Lazarus-B, and learns the truth. Lazarus-B's people discovered how to pass through the negative magnetic corridor that both connects and protects the two universes. When this happened, Lazarus-A couldn't bear the knowledge that he had a duplicate, and resolved to destroy his opposite. He is mad and doesn't care if this causes the destruction of two universes. Lazarus-B and Kirk realize he must be stopped: if Kirk can force Lazarus-A into the corridor, Lazarus-B can hold him there, and Kirk can destroy his spaceship – which will also destroy Lazarus-B's spaceship. Access to the corridor will be sealed forever and both universes will be safe, but the men named Lazarus will be at each others' throats for the remainder of eternity. Kirk goes back through the corridor and fights in hand-to-hand combat forcibly throwing Lazarus-A into the "dimensional door." Kirk heads back to the Enterprise, ordering the Lieutenant Leslie to bring the ship's phasers to target the inter-dimensional ship. The two Lazaruses meet once more and fight as phaser beams vaporize the ship, sealing the two for all of eternity, caught together, between universes. Kirk ruminates on the fact that the two Lazarus are going to be at each other's throats for all time and wonders how it would be. Spock reminds Kirk that the universe is now safe. "For you and me. But, what of Lazarus? What of Lazarus?"

"Captain's log, stardate 3087.6. While investigating an uncharted planet, the Enterprise, and at least this entire quadrant of space, has been subjected to violent, unexplained stress and force. Sensors have reported the presence of a Human being on the planet below who might be connected with the phenomenon. With my first officer and a security team, I have set out in search of him."

"Captain's log, stardate 3088.3. We continue to orbit the dead planet, which seems to be the source of the phenomenon which has struck the Enterprise, and all sections of the galaxy, once again. As for Lazarus, the story he tells me about the humanoid continues to trouble me."

"Captain's log, stardate 3088.7. We are no closer to finding an answer to the strange phenomenon than we were at the beginning. Not only have two of my crewmen been attacked, two of our dilithium crystals are missing, and without them, the Enterprise cannot operate at full power. They must be found."

The original script called for a romantic entanglement between Charlene Masters and Lazarus that was eventually cut due to Roddenberry considering it too similar to the romance between Khan and McGivers in "Space Seed". As stated by Roddenberry in a Season One memo: "In both 'Space Seed' and this story, we have a crew woman madly in love with a brawny guest star and flipping our whole gang into a real mess because she is in love... do they have to do [this] in two of our scripts?" [1]

After Barrymore failed to show up on the set, director Gerd Oswald decided to shoot scenes which didn't involve his character. On the second day, it was decided to either shut down production and scrap the episode overall or find a replacement. Robert Brown was literally dragged in to the set, right after he agreed to play the role. He recounted the filming to be very tight and tense. [2]

There is no officer played by Larry Riddle as noted in the Star Trek Concordance. Lieutenant Larry Riddle was Charlene Masters' jealous boyfriend in the first draft of the script. [3]

For reasons unknown, the standing engineering set was not used in this episode. When Lazarus attempts to sabotage engineering, he does so to an entirely new (albeit smaller) set.

Along with "Friday's Child", this is one of the only two episodes where outdoor planet scenes were filmed both on Desilu Stage 10 and on location (both times at Vasquez Rocks). Originally, all planet-side scenes were scheduled to be filmed on location, but due to the turmoil during production, director Gerd Oswald couldn't finish shooting at Vasquez. Matt Jefferies and the art department prepared a spot on Stage 10 which could accomodate the missing "alternate universe" sequence. [4]

Although Lazarus's spacecraft resembles a flying saucer, James Blish describes it as "cone-shaped" in his novelization of the episode in Star Trek 10.

Periodically throughout the episode, the two versions of Lazarus exchange places. One of them has a wound or bandage on his head which McCoy treated: this is the "insane" Lazarus from our universe; the other is his rational counterpart from the antimatter universe.

Lieutenant Masters wears no braid on the sleeves of her uniform, but she is addressed as a lieutenant. A similar wardrobe error happened in "Space Seed" when Lieutenant Marla McGivers also is "braidless."

Although Masters works in engineering, she wears the blue uniform of the Science/Medical branch.

The shot of the Enterprise destroying Lazarus' ship is unique on three counts. First, it is the only time the Enterprise is seen from behind as it fires phasers. Second, it is the only time that the ship fires a single beam (as opposed to the usual two). Finally, it is the only time that the phasers make no noise – at least when the beam is seen in space.

The footage of the two Lazaruses fighting was created by filming two stuntmen fighting in a smoke-filled room with orange and purple walls, then double-exposing its color negative footage over an astronomical photograph of the Trifid Nebula.

A still image in the closing credits of "The Squire of Gothos" shows the corridor between universes set unaltered by the effects and double exposure. Titled at a 45 degree angle, Shatner stands ankle deep in smoke in a near pose of the crucifixion, falling back into a purple corridor, where an orange line draws the horizon to a vanishing point.

This is the first time that live two-way communication with Starfleet Command is depicted. In previous episodes, communication with Starfleet Command was through delayed radio messages.

Unlike in the earlier "Mudd's Women", dilithium crystals are portrayed here as translucent amber slabs, which conveniently fit in the energy panels of Lazarus' ship. The universality of the amber-slab dilithium crystal mount connector as being common to both the Enterprise and to Lazarus' timeship, suggests a commonality in the manufacture and sourcing of at least its dilithium crystal converter assembly. There is also no mention in "The Alternative Factor" of bypass circuits being fused beyond useabilty as a power-conversion alternative, the existence of which were mentioned to bolster the direness of the need for replacement crystals in the storyline of "Mudd's Women". Dilithium crystals, in their natural state, however, are depicted as resembling quartz crystals in both "Mudd's Women" and "Elaan of Troyius", suggesting that the amber-slab devices depicted in "The Alternative Factor" are themselves some kind of mounting structure, the translucent glow meant to depict the power flow somehow being transformed by being focused through the crystal or crystals contained within. The amber slabs are, however, explicitly referred to in dialogue as being the crystals themselves.

Depending on which version of this episode you watch, the closing stills change. The original syndicated version and the VHS version show the still as the Enterprise leaving the Earth-like planet from "Miri", however, the Sci-fi Channel and DVD version show the still as just a blue planet, possibly Rigel 12 from "Mudd's Women" or Starbase 11 from "Court Martial".

Lazarus never introduces himself by name to Kirk, yet he calls him by name during the first planet search.

At the beginning of "Act Three" in the conference room, when Lazarus is accused of attacking the engineering officers, his mustache and beard appear less "full," with less hair than previous seen. Later, when he beams to the planet with the landing party, his mustache and beard has returned to its "fuller" state.

The Agony Booth website included this episode among "The Worst of Trek". In their recap, they write that in the episode, "Very little actually happens, and what little that does comes about only because Kirk and Company are written to act in such a way that can only be described as severely brain damaged." The reviewer continues, "I never thought I'd say this, but this episode is making "Spock's Brain" look pretty goddamn good right about now!" He concludes, "this is one of the most poorly constructed fifty minutes I've ever seen. An almost impossibly incoherent script, a damp squib of a finale, and some horrible editing make this one of the true stinkers in the Trek universe." Also, he mentions that "[John Drew] Barrymore didn't show up for filming. Given the script, I can't say I blame the fellow. The rest of the cast should have done the same thing, to be perfectly frank." [5]

"The Alternative Factor" was the forty-ninth episode of the remastered version of The Original Series to air. It premiered in syndication on the weekend of 1 December2007 and aside from the standard CGI replacement footage of the Enterprise and the planet-of-the-week, this episode also featured several new, modest effects shots of the alternative warp effect, as well as phaser and transporter effects.

Original rendering of planet...

...and its remastered counterpart

Original rendering of the planetary radiation signature on viewscreen...

...and its remastered counterpart

Original rendering of the battle between Lazaruses in the alternative warp...